Rabbit thumping at Guinea pigs

Hi guys, so yesterday I got out my guinea pigs play pen, which used to be sprinkles but she just has free reign now, I set it up in the living room where my bunny lives. We've got wooden floor which are slippery so Sprinkles stays on the massive hearth and the big rug and jumps on the sofa. The living room is big so I put the play pen on the wooden floor with a towel down for the Guinea pigs. It was about a metre away from the rug Sprinkles is on. Anyway the pigs started making noises, exploring their pen and she started thumping her foot and wouldn't stop!! I took the guineas in another room for cuddles with my mum and she was still stomping so I moved the playpen out of her sight and she still was thumping for about 30mins after! Does she not like them and sees them as a threat or was she grumpy? I don't how why she did it. I was comforting her and stroking her to soothe her but it continued. But the guineas live upstairs and are very vocal so she can easily hear them and isn't bothered. Can they not be in the same room at all or will they get used to each other? I know guinea pigs and rabbit can't live in the same cage but can they not even be in the same room? I don't want her to be stressed but I'd like to be able to watch over her and the guinea pigs while they play. I was just wondering if that was possible or should I just do it separately from now on?

I think they will get used to each other, the rabbit was probably moody as she feels the guinea pigs are invading her territory.
I do believe if the rabbit see's them regularly eventually she will just ignore the fact the guinea pigs are there.